The abundant and diverse calcareous nannofossil assemblages found in the sediments of two ODP cores from the Western (Site 975B, South Balearic Basin) and Eastern (Site 969B, Mediterranean Ridge) Mediterranean Sea have been taken into account for the paleoenvironmental reconstruction of the surface water conditions during the first 490kyrs immediately following the end of the Messinian Salinity Crisis, chronostratigraphically settled at 5.332Ma. The areal distribution of the calcareous nannofossils is closely linked to their ecological and environmental affinities, mostly driven by temperature, salinity, nutrients or other chemical parameters of the water masses. Hence, taxa (or groups of taxa) showing well-known ecological behaviors were considered, and different environmental evolutions were recognized for the two sectors of the Mediterranean Basin during the early Zanclean (early Pliocene). Specifically, in the Western Mediterranean a switching from a warm and oligotrophic water environment, showing normal open-marine conditions, to a colder and eutrophic one, characterized by a decrease in salinity rates and the development of a more restricted environment, can be recorded. Conversely, in the Eastern Mediterranean the environmental setting immediately following the MSC is indicative of temperate waters and normal open-marine conditions, which evolves, in the younger layers, to a warmer environment characterized by high salinity rates and typical of a restricted marine context. The timing of the environmental transitions recognized at the two sites has been set through the Principal Component Analysis. Taxa and groups of taxa reflecting precise ecological affinities have been handled together and a transition interval have been defined between 5.20/5.15Ma and 5.06/4.98Ma, and between 5.10Ma and 4.92Ma in the Western and Eastern Mediterranean, respectively. •We considered the calcareous nannofossil assemblages of two Mediterranean ODP sites.•We outlined the surface water properties based on nannofossil paleoecology.•We showed the differences between West and East Mediterranean in the early Pliocene.•The environmental parameters driving the changes were emphasized by the PC analysis.•We rebuilt the 490kyrs-environmental evolution of two key-areas of the Mediterranean.